NGS Scientific Software Applications

Many sites on the NGS make available a range of Scientific Software. These applications are available for use via the UI/WMS resource broker or via globus commands. The table below shows which applications are available at which sites.

The UI/WMS can select the most appropriate site for you or you can request your job to run at a specific site. The links in the table will take you to pages showing you how to submit grid jobs to use the application from the UI using the WMS, the NGS portal, or via direct globus commands. In some instances the software may not be fully grid enabled and may need to be run by logging into the site first. These documentation pages give instructions for how to do this where appropriate.

Click on the categories below to see the applications available. Click on an application to see which versions are available and at which NGS sites. Click on the Documentation links to see how to run that application on the NGS. Click on a site name, on the right hand side, to see which applications are available at that site.

Application Categories

AstroPhysics Overview
- CosmoMC Documentation
  - 200806 STFC-RAL
- Gadget2 Documentation
  - 2.0.3 Oxford STFC-RAL
BioInformatics Overview
- Beast Documentation
  - 1.5.3 Leeds Oxford
- EXONERATE Documentation
  - 1.4 STFC-RAL
- Emboss Documentation
  - 4.1.0 STFC-RAL
  - 6.0.1 STFC-RAL
- FASTA Documentation
  - 34.26.5 STFC-RAL
- GROMACS Documentation
  - 3.3.1 Leeds Manchester Oxford STFC-RAL
  - 4.0 Leeds STFC-RAL
  - 3.3.3 Oxford Super Computing Westminster
  - 4.0.7 Oxford Super Computing
  - 4.0.5 Westminster
- Mrbayes Documentation
  - 3.1.2 Oxford Super Computing STFC-RAL
  - 3.1.2.1 STFC-RAL
- NAMD Documentation
  - 2.6 Leeds Manchester Oxford Oxford Super Computing STFC-RAL
  - 2.7b1 Leeds Oxford STFC-RAL
  - 2.7b2 Manchester
- NCBI BLAST Documentation
  - 2.2.18 Glasgow Scotgrid Leeds STFC-RAL svr026.gla.scotgrid.ac.uk
  - 2.2.17 Oxford STFC-RAL
  - 2.2.16 STFC-RAL
- NCBI BLAST Toolbox Documentation
  - 25032007 STFC-RAL
- SIESTA Documentation
  - 2.01 Leeds Manchester Oxford STFC-RAL
  - 3.0 Oxford Super Computing
- mpiBlast Documentation
  - 1.4.0 STFC-RAL
BioMedical Overview
- GATE Documentation
  - 3.1 STFC-RAL
  - 3.1.1-1 STFC-RAL
  - 3.1.1-2 STFC-RAL
  - 4.0.0 STFC-RAL
Chemistry Overview
- AMBER Documentation
  - 10 Leeds
  - 10.0 Leeds STFC-RAL Westminster
  - 9 Leeds
  - 9.0 Leeds STFC-RAL Westminster
- Autodock Documentation
  - 4.0.1 Leeds Oxford STFC-RAL Westminster
  - 4.2.2.1 Leeds Oxford STFC-RAL Westminster
- Autogrid Documentation
  - 4.0.0 Leeds Oxford STFC-RAL Westminster
  - 4.2.2.1 Leeds Oxford STFC-RAL Westminster
- CASTEP Documentation
  - 4.3 Leeds STFC-RAL
  - 5.0.1 Leeds Manchester STFC-RAL
  - 4.3-r3 Manchester
  - 4.2 STFC-RAL
- Castep Utilities Documentation
  - 4.3 Leeds STFC-RAL
  - 5.0.1 Leeds Manchester STFC-RAL
  - 4.3-r3 Manchester
  - 4.2 STFC-RAL
- DL_POLY 2 Documentation
  - 2.19 Leeds STFC-RAL
  - 2.16 RAL SCARF STFC-RAL
  - 2.20 RAL SCARF STFC-RAL
- DL_POLY 3 Documentation
  - 3.09 Leeds STFC-RAL
  - 3.06 RAL SCARF STFC-RAL
  - 3.10 RAL SCARF STFC-RAL
- Dock Documentation
  - 6.1 STFC-RAL
- Firefly Documentation
  - 7.1.G STFC-RAL
  - 7.1.H STFC-RAL
- Firefly/PC-GAMESS Documentation
  - 7.1.5 Leeds
  - 7.1.C Leeds STFC-RAL
  - 7.1.E Leeds STFC-RAL
  - 7.1.11 STFC-RAL
  - 7.1.4 STFC-RAL
  - 7.1.9 STFC-RAL
  - 7.1.D STFC-RAL
  - 7.1.F STFC-RAL
  - 7.1.G STFC-RAL
- GAMESS (US) Documentation
  - 7.0 STFC-RAL
- GAMESS-UK Documentation
  - 7.0 STFC-RAL
- GROMACS Documentation
  - 3.3.1 Leeds Manchester Oxford STFC-RAL
  - 4.0 Leeds STFC-RAL
  - 3.3.3 Oxford Super Computing Westminster
  - 4.0.7 Oxford Super Computing
  - 4.0.5 Westminster
- GROMACS (AMBER forcefields) Documentation
  - 3.3.1 Leeds
  - 4.0.3 Leeds
- Gaussian Documentation
  - E.01 RAL SCARF STFC-RAL
  - C.02 STFC-RAL
- Gaussian Utilities Documentation
  - C.02 RAL SCARF STFC-RAL
- Gaussian09 Documentation
  - A.02 RAL SCARF STFC-RAL
- Gaussian09 Utilities Documentation
  - A.02 RAL SCARF STFC-RAL
- Gulp Documentation
  - 3.1 STFC-RAL
- LAMMPS Documentation
  - 070622 Leeds Manchester STFC-RAL
  - 080521 Leeds STFC-RAL
  - 090417 Leeds STFC-RAL
  - 090714 Manchester
  - 070709 Oxford
  - 070810 STFC-RAL
- NAMD Documentation
  - 2.6 Leeds Manchester Oxford Oxford Super Computing STFC-RAL
  - 2.7b1 Leeds Oxford STFC-RAL
  - 2.7b2 Manchester
- ORCA Documentation
  - 2.6.35 Oxford Super Computing
  - 2.7.0 STFC-RAL
- Schrodinger Suite Documentation
  - 2009u2 Leeds
- Siesta Documentation
  - 2.01 Leeds Manchester Oxford STFC-RAL
  - 3.0 Oxford Super Computing
- VASP Documentation
  - 4.6 STFC-RAL
- WIEN2K Documentation
  - 08 Leeds
Data Analysis Overview
- GNU Plot Documentation
  - 4.2.2 Leeds
- IDL Documentation
  - 7.0 RAL SCARF STFC-RAL
- MGL Tools Documentation
  - 1.5.2 Westminster
- Matlab Compiler Runtime Documentation
  - R2008a.glnx86 Leeds
- Octave Documentation
  - 2.1.57 Glasgow Scotgrid STFC-RAL svr026.gla.scotgrid.ac.uk
  - 2.1.73 Leeds Manchester STFC-RAL
  - 3.0.0 Leeds Manchester STFC-RAL
- POV-Ray Documentation
  - 3.6.1 Leeds Oxford
- R Documentation
  - 2.6.2 Glasgow Scotgrid Oxford svr026.gla.scotgrid.ac.uk
  - 2.6.0 Leeds Manchester RAL SCARF STFC-RAL Westminster
  - 2.9.2 Oxford Super Computing
  - 2.4.1 STFC-RAL
- Root Documentation
  - 5.12 STFC-RAL
  - 5.14 STFC-RAL
- Sabre Documentation
  - 4.0 STFC-RAL
  - 5.0 STFC-RAL
  - 6.0 STFC-RAL
- SciPy Documentation
  - 0.6.0 Leeds
- Weka Documentation
  - 3.4.9 STFC-RAL
Engineering Overview
- Abaqus Documentation
  - 6.9 RAL SCARF STFC-RAL
  - 6.6.1 STFC-RAL
  - 6.7.1 STFC-RAL
  - 6.8 STFC-RAL
- Fluent Documentation
  - 6.3.26 Leeds
- OOMMF (Object Oriented MicroMagnetic Framework) Documentation
  - 12a3 Leeds
  - 12a4pre Leeds
Image Analysis Overview
- Bsoft 64bit Documentation
  - 1.5.4 Leeds STFC-RAL
- IDL Documentation
  - 7.0 RAL SCARF STFC-RAL
- POV-Ray Documentation
  - 3.6.1 Leeds Oxford
Uncategorised
- BEAMNRC
  - 2007 Leeds
- BLAST
  - TOOLBOX.NCBI Glasgow Scotgrid Oxford svr026.gla.scotgrid.ac.uk
  - TOOLBOX.NCBI-test.sh Glasgow Scotgrid svr026.gla.scotgrid.ac.uk
  - TOOLBOX.NCBI.25032007 Glasgow Scotgrid svr026.gla.scotgrid.ac.uk
  - TOOLBOX.NCBI.20070822 Oxford
- BSOFT32
  - 1.5.4 Glasgow Scotgrid Leeds STFC-RAL svr026.gla.scotgrid.ac.uk
- CCP4
  - 6.1.2 Oxford
- DOCUTILS
  - 0.5 Leeds
- EM3DR2
  - 2.0.2 Glasgow Scotgrid Leeds STFC-RAL svr026.gla.scotgrid.ac.uk
- GAMESS-US
  - R1-10Apr08 Leeds
  - R1.11Apr08 STFC-RAL
  - R6 STFC-RAL
- HARC
  - CLIENT Leeds Manchester Oxford
  - CLIENT.1.9.3 Leeds
  - CLIENT.1.9.5 Leeds Manchester
  - CLIENT.2.0.0 Leeds Oxford
- JAVA
  - 1.4.2 Leeds Westminster
  - 1.5.0 Leeds STFC-RAL Westminster
  - 1.6.0 Leeds STFC-RAL Westminster
- MPI
  - START Leeds STFC-RAL
  - START.0.0.58 Leeds
  - BLAST Oxford
  - BLAST.1.5.0-pio Oxford
- MPIG
  - 1.0.6-200710190227 Leeds
- PFT2
  - 2.0.4 Glasgow Scotgrid Leeds STFC-RAL svr026.gla.scotgrid.ac.uk
- PYTHON
  - 2.6 Manchester
- PYTHON26
  - 2.6.2 Leeds
- VMD
  - 1.8.6 Westminster
- 1

Sites

Glasgow Scotgrid

Leeds

Manchester

Oxford

Oxford Super Computing

RAL SCARF

STFC-RAL

Westminster

lcgce05.gridpp.rl.ac.uk

svr026.gla.scotgrid.ac.uk

Applications Support

The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.

Acknowledgements

Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.

Primary links

NGS Scientific Software Applications

Application Categories

Sites

Applications Support

Acknowledgements

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